rs760395622

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005601.4(NKG7):​c.476G>T​(p.Arg159Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R159G) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

NKG7
NM_005601.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.32
Variant links:
Genes affected
NKG7 (HGNC:7830): (natural killer cell granule protein 7) Predicted to be integral component of plasma membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.091578156).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NKG7NM_005601.4 linkc.476G>T p.Arg159Leu missense_variant Exon 4 of 4 ENST00000221978.10 NP_005592.1 Q16617

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NKG7ENST00000221978.10 linkc.476G>T p.Arg159Leu missense_variant Exon 4 of 4 1 NM_005601.4 ENSP00000221978.4 Q16617

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000194
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.27
T
BayesDel_noAF
Benign
-0.63
CADD
Benign
0.50
DANN
Benign
0.88
DEOGEN2
Benign
0.084
T;.;.
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.034
N
LIST_S2
Benign
0.66
T;T;T
M_CAP
Benign
0.0067
T
MetaRNN
Benign
0.092
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.6
L;.;.
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-2.3
N;.;.
REVEL
Benign
0.14
Sift
Benign
0.11
T;.;.
Sift4G
Benign
0.30
T;T;T
Polyphen
0.0040
B;.;.
Vest4
0.11
MutPred
0.39
Loss of disorder (P = 0.0464);.;.;
MVP
0.23
MPC
0.13
ClinPred
0.40
T
GERP RS
-7.7
Varity_R
0.043
gMVP
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs760395622; hg19: chr19-51875053; API